Auto+locker all the way.
Sure manual shifting is fun in the right circumstances, but manual clutches SUCK.
* They suck for towing (Autos have higher towing capacity, all truck towing capacities are rated for Auto because it;s quite a bit higher than a standard clutch allows)
* They suck for hill climbing, rock crawling and tricky offroad situations. (Seen manual users nearly burn their cluctch out on the trail numerous times and have to sit back and wait for it to cool off for 20-30 minutes before continuing. NO THANKS. Not to mention almost always having a much harder time on obstacles than autos)
* They suck for traffic which I drive in every day...
Had manuals all my life till an auto Taco and now my auto 4R and would NEVER go back. The "fun" stops quickly and too often and just becomes a real PITA fast in a lot of situations... In a dune buggy or baja bug racing around the desert and nothing else? Sure. In my 4R? No way.
On a 3rd gen, the 5 speed is better for towing, no question. I've owned 3 autos and one 5 (all 5VZ.) The 5 speeds have an extra short 1st to get rolling, and after that you have almost no heat generation that you'd get with the auto, and way more control, especially from engine braking. Don't need to worry about O/D either. A 3rd gen 5 speed with rear airbags & tundra brakes is actually a pretty good setup.
There's a reason most hardcore tow rigs are manuals. They don't make them anymore in lighter duty trucks (Ford SuperDuty etc.) because a huge majority of those customers don't actually tow with them, and manual volume would be small. Big rigs, however...